Code: Doctor
by Lyoko498
Summary: One evening Franz Hopper receives a visit from an old friend. Years afterwards the Doctor runs into a familiar young lady
1. Prologue: Part 1

Code: Doctor

(The story takes place before Anthea, Aelita's mother was kidnapped, so Aelita's a little girl in this. I hope you enjoy it. Lyoko498)

Franz Hopper was sitting in a chair, his daughter on his lap, as he read her a story before bed. She held Puck in hand, her beloved doll being something to hold on too, as her father read The Modern Prometheus by Mary Shelley, otherwise known as Frankenstein.

"Satan has his companions, fellow-devils, to admire and encourage him," read Franz, wishing his daughter wasn't as smart as she was. Since he started reading this book to her, Franz and his wife Anthea, would wake up the next morning to seeing a little pink head in their bed. But Aelita was interested after finding it in her father's library.

A knock came on the door. "I wonder who that could be?" questioned Anthea, standing up from the chair she sat on and walked towards the door. It creaked as she opened it, stopped by the chain lock. Before her was a raggedy man. His hair was brown and a tad out of control, he wore dark trousers, a white and brow striped shirt and a tan over coat and a bow tie.

"Hello." said rang the British voice cheerfully. "May I come in? I have very important business to speak about with your husband." He flashed out a piece of identification paper, "I worked with him, and I _must_ see him. Now, nothing is wrong, not currently."

The man's eyes peered around to the left and he saw Franz and Aelita, "Franz! Ooh I see you got a little girl now! Hi there!" Aelita looked up to her father and asked him who the man was.

"Uh, he's a former associate of mine. Um, let him in Anthea." Reluctantly she undid the chain, and opened the door to the strange man. "Thank you very much Anthea." the man smiled.

He turned to Aelita, "And who might you be?"

She smiled and answered, "Aelita."

"You don't say? Like the rose? Well it suits you. Oh you're so cute. Anyway, Franz, I need to talk to you in private about a pressing matter."

Franz looked back down at his daughter and back to the man, "Well I'm kind of busy reading to my daughter."

"I see, mind if I join? I love a good book." laughed the man , taking a chair in the kitchen, moving it to the living room. Anthea looked at the strange man. She wasn't upset with him in any way, but she was curious about him, as if something was not quite right with him.

So Franz read a little more, as the man then quipped, realizing what was read, "Really Franz? You're reading Frankenstein, or The Modern Prometheus to your young daughter?"

"Well she found it and was instantly interested in it." Franz defended.

The man shrugged his shoulders and sat back, listening to the story. After a few more minutes, Franz was done reading. The man smiled at his daughter, before looking at his guest, who was also smiling, but a more nostalgic smile.

"Mary Shelley was a wonderful writer, don't you agree?" said the guest. Aelita was hugging her doll, the book persisting to scare her.

The guest kneeled down and gently grabbed the girl's shoulder and said, "'ey don't worry about the story. It's only that a story. The Creature isn't real and it can't hurt you. Now, why don't you go upstairs, say whatever prayers you say, and go to sleep. I assure you that you'll be fine."

The guest kissed her head and gently lead her to her room.

With their daughter and the man gone Anthea asked her husband, "So, who is he?" Franz groaned slightly. He wanted to not mention _him_ to his wife. Not that he was a bad man, as she now just witnessed. But Franz sighed and answered, "And old friend of mine, who goes by the alias of "The Doctor". We worked together on something when I was working on _that project_."

She nodded and said, "I understand." Just then the man came creeping away from Aelita's room, tip-toeing his way to them, putting a finger to his lips. "Shhhh, she's asleep. So precious."

Anthea then asked, "So you needed to talk to Franz about something?" The Doctor's face quickly changed from soft and kind to hard and somewhat stern. "Yes, it's about _that project_ Franz." Anthea pretended to look at a watch, saying, "Oh, well I should also start getting ready for bed. See you in a bit Franz?"

"Yes Anthea.." And like that she walked to her room. Now all that remained in the room was Franz Hopper and the mysterious man known only as The Doctor. Franz noticed that the Doctor was upset, he saw that in his eyes, but also he saw great sadness.

"Franz how could you?"

Franz was confused, "What are you talking about, you told me to sabatage Project Carthage?"

"Not _that_ project Franz!" snapped the Doctor, "My TARDIS' scanners noted that this days have been rewinded, the largest "replayed" being over 2,546 times!" Franz was shocked The Doctor noticed. "I don't know what you're talking about Doctor," Franz lied, walking to the kitchen, grabbing a glass, filling it with milk (Anthea hated it when he drank alcohol before he went to bed.)

"Ooh but you do!" The Doctor replied, "You don't think I can recognized a hyperspacial chronotonic reversal wave? Which is still expanding across the universe might I add! Over 2000 of these time reversing waves, forcing planets to go through temporal instability, granted in this case it's not cataclysmic but it's still a big deal!"

Franz snapped at the Doctor, "I have no choice!" After the two men glared at each other for about three minutes, Franz finally spoke, "I'm building something important Doctor. Something that'll bring Project Carthage to it's knees."

The Doctor questioned, "What? What have you done Franz?" Franz put his glass to his lips and took a sip. Franz could understand The Doctor's concern. But in the end, the rewind function might never be used again.

"I created a quantum supercomputer, Doctor. And within it… a sanctuary." Franz answered, trying to regain his cool. The Doctor looked shocked, "No." He turned around, went back to the living room, repeating the word "No." He was worried, as he concluding by saying, "This is not good, on a list of things that are good, this would be near the bottom!"

Franz inquired, "How? The men in black are after me and my family Doctor! We need a place to be safe!" The Doctor turned to face him and stopped his pacing, "Don't tell me you did what I think you did…"

Franz answered, "I created a virtual world. Originally called XANADU, but eventually, it evolved beyond that, and I called the perfected version LYOKO. I put in a program, called X.A.N.A. to use structure I created, towers, to destroy Project Carthage. I have digital avatars ready. A whole world to live in, and hide from the wrath of my former associates."

The Doctor grabbed Franz's arms firmly, sternness replaced by worry, "Franz! You're playing God! Do you know how many times I've seen that happen? Every single time, I've witnessed a factor, something that's almost bound to happen. It will betray you, beat you…kill you. The Prometheus Effect…The Lucifer Factor…"

Franz knew this was irrelevant but from all his time of knowing The Doctor, the allegories were a tad strange and said, "I always thought you were atheist."

The Doctor shrugged and corrected, "Transtheist actually…That's besides the point! Franz, you're a loyal companion, and a good man. I'd hate to see something bad happen to you because of a stroke of insanity!"

A small noise came from the corner, causing both men to look to the side. There stood Aelita, hugging Puck, scared. The Doctor let go of Franz, letting him pick up his daughter. "Did he hurt you Daddy?" Aelita asked her father.

Franz shook his head, "No, no. This man is my friend Aelita. He wouldn't hurt me on purpose. I know he means well, but I fear that he is a tad…overprotective on a little project I'm doing." The

Doctor walked towards the girls and continued, "That's right Aelita. You're father is a good man, and I'm just concerned about something he's doing. I'm not going to hurt him, you, or anyone else."

Franz walked Aelita to her room, tucked her in, and returned to the living room.

"Please Franz," said The Doctor, concern filling his voice even more, if that were possible. Franz sadly shook his head, "I'm sorry Doctor. But this is something I must do." With that The Doctor nodded, "Alright Franz. I understand. It's a good idea in your head and I can see why. But please remember this one thing Franz, when I say "Run," I don't mean "Run away from your problems."

Franz nodded, "I know Doctor, I know." The Doctor hugged the man, surprising Franz, but he eventually returned it.

And with that the Doctor walked out the door and returned to his little blue box across the street. A strange noise emitted from it, fading, fading, until it was finally gone.

(I was considering extending this to a full story, but I'll let you all decide on that. I hope you liked this story, and maybe would like to see it continued too. :) If you didn't like it, I'm sorry. J Lyoko498)


	2. Prologue: Part 2

(A/N: While I only got three reviews at the time of this chapter, so far they are positive and encouraging…and, well 3 times a charm :P. So, I'll try to expand it a bit more and see how it goes. Hope you enjoy! Lyoko498

The Doctor was fiddling around with the console, Rory and Amy in their room doing…whatever it was they did, The Doctor didn't really want to know. He then noticed that the defenses were down. "Oh, might want those shields up," he whispered to himself, "Don't want to run into the seventh me." He pressed a few buttons, flipped a couple of switches and turned that thing and the shields were up.

There was a low, dull beeping came from the monitor.

"Hmm?" The Doctor pulled the screen to him.

"SPACIAL-CHRONOTONIC REVERSAL WAVE DETECTED."

'Waldo!' The Doctor thought, using his friend's real name. He sprung into action, turning that crank, pulling wires and pushing that thing there, The Doctor redirected the TARDIS towards France.

CRASH!

"Damn! The Wave is causing turbulence. But we can do it old girl!" he said to his TARIDS. Amy stumbled and fell on the floor by the door leading to the hallway.

"Uhg, Doctor! What are you doing!" she yelled, the turbulence getting worse.

"I detected something going on in France 1994 a friend of mine might be in serious trouble why are you wearing a bathrobe?"

Amy looked down and answered, "Rory and I went swimming."

"Oh you finally found it I see, anyway!, tell Rory to hold on to something!" Amy nodded and ran back to the pool. The Doctor looked at the console again and said, "Well…GERONIMO!"

The TARDIS crashed and skid, before it came to a halt at a black iron fence, which bore the plaque "Hermitage". The TARDIS was on its side, to The Doctor literally had to climb out the door. He jumped out and sprinted across the lawn.

He tried the knob, locked. From his pocket The Doctor pulled out the sonic-screwdriver, clicked the button. It lit up green, gave its distinctive whir, and the door was unlocked.

"Fra-whoa, you're not Franz Hopper!" The Doctor bellowed, only to bring his voice down to normal volume as he saw a small group of men in black suits. The man closest to him turned, and pulled out his pistol.

The Doctor's arms shot up, "Ey, calm down will you!"

The man holding him hostage made a gesture with his head, implying that he wants one of them to watch him. The Doctor then said, "Well you lot seem to be pretty busy right now, so I'm just going to go, that way and leave." As he tried to walk back, the new "guard" threw a punch towards The Doctor.

He side stepped grabbed the black clad man's arm, and threw him into the door, then proceeded to kick him through the door.

"Oooh! Venusian Aikido! Haven't done that in 8 incarnations! How exciting!" laughed the Doctor, moving on to the next agent, who promptly tricked to sidekick him, only for the Doctor to jab at several pressure points, paralyzing his leg. The Doctor then squeezed where the shoulder meets the neck and the man fell.

Two more men came downstairs, and unlike the other two, they deiced to do something remotely intelligent and actually _used_ their guns. The Doctor ducked for cover behind a couch. "Well this escalated fast," he muttered to himself, "But where there's a will, there's a way."

The Doctor peered over the couch while the men reloaded, they had earpieces for communications. "Ah ha!" he whispered to himself, dragging the unconscious agent by his stiff leg. The ear piece was now in the palm of his hand, and aimed the sonic-screwdriver at it. "Well here goes nothing…" The Doctor felt a bit of his pervious self come up and finished with "Allons-y!" He clicked the button.

The two agents dropped their guns and grabbed their heads as a high-pitched shriek blasted through their eardrums, forcing them to the ground. "Well that ought to take care of you." whispered The Doctor as he rushed along to a door. "Locked," he whispered, "You mad genius Franz. But not smart enough." Another click of his screwdriver and the door opened.

A tunnel bore out of the house. "I knew it." He sprinted back to the TARDIS and yelled inside, "Don't move! I'll get back to you in a moment!" and snapped the doors shut and locked them before either could respond. He sprinted down the tunnel and ran as fast as he could.

It took about half an hour (much longer to a time traveler) before he found a sewer lid. "Yes!" The Doctor climbed a ladder and pushed it out of his way. A factory loomed over him. "So _that's_ where you built it Franz…" The Doctor muttered to himself, crawling out of hole he was in and sprinted across the bridge to the large gap of an entrance.

He stopped when he saw the stairs ended in the air, "Well that's inconvenient oh ropes are right there." The Doctor tightly grabbed on the ropes and shouted, "GERONIMO!" as he swung to the ground. "Ah! Elevator! Good!" The Doctor clicked the down button, but it didn't move.

"I'm detecting a patter here," The Doctor said to no one in a hurried voice, pulling out his sonic-screwdriver. It flashed green and the elevator powered up and opened. He rushed in, turned around and hit the button again, repeatedly, "Come on! Come on!" Finally the elevator started to go down.

"Hurry up!" The Doctor shouted, upset with the speed it was moving at. At last it stopped and The Doctor was, surprised to say the least. Inside the room was a giant hologram of a strange world.

The Doctor walked towards it, amazed that Franz managed to do it, he listed the biomes, the sectors, "Forest," he said, pointing to his current right, moving to the lowest one, "Desert," the next one, "Artic," and the top one, "Mountain." He originally thought that that was it, but as he was about to go to the monitor he looked again, and concentrated on the orb in the middle. He leaned towards it and said, "Carthage…the ultimate irony."

He went to see the monitor of the computer. "Incredible, He managed to perform atom to virtual particle transference, based on Yith technology, transferring the mind to another place in space-time, but unlike the Great Race, they maintain their bodies, except reconstructed into a virtual avatar…"

On the bottom of the screen was a yellow sticky-note. It read as the following:

_**Doctor**_

_**I know that you'll find out about the time reversal again. To put you up to speed, I regret to say the men in black have kidnapped my beloved Anthea…**_(there were some tears drying on the note)_** but Aelita and I are safe, but they found us, so I have to send us both to LYOKO. I'm sorry Doctor, I'm so sorry. But now I have but one request, one more favor. X.A.N.A. has gone rogue, and I employed a program to keep him in check, please make sure it can last! I fear X.A.N.A. might hack it and unleash itself upon the world, please Doctor! For Peace! For Sanity!**_

The Doctor sat down instantly and begun adding more "firewalls" and "blockers", "Earth computer's are a piece of cake, usually. But credit where it's due my friend, you sure made this hard for me." he muttered as his fingers scrambled across the keyboard, adding more and more codes and systems to keep X.A.N.A. from escaping. He even added some Gallifreyan codes, something that'll take X.A.N.A. forever to crack.

"There," said The Doctor, imagining Franz was standing beside him, "There's no way it…he, can get out," he continued, giving X.A.N.A. a pronoun, feeling that if X.A.N.A. went rogue, he was probably sentient and should be treated as such.

The Doctor went to the elevator, knowing what he should do. He hit the down button again, and went to the bottom room. There stood a massive black and gold machine. "The Quantum Supercomputer." The Doctor said to himself, walking towards it, opening a panel with the sonic-screwdriver, seeing a handle.

There's one thing Franz wasn't, and that's foolish. Strokes of stupidity and insanity, definitely, but not foolish. "You preserved your world," he whispered, "You knew I was going to do this, so you and Aelita could be sure you'll still be alive." The Doctor grabbed the switch.

"Good bye Franz, I hope I can see you again one day."

The yellow metal ceased to glow and the computer retracted to the floor.

He walked back to the elevator, looked up at the roof of it, The Doctor said, looking back down at his sonic-screwdriver, "Well, while I have it out…"

The elevator zipped back up to the main corridor. Granted in about, say 10 years, it'll slow down a tad, but still better than what it was like before.

The Doctor clicked the button on the sonic-screwdriver again, and in a matter of seconds, the TARDIS materialized before him. Rory opened the door and asked, "Doctor? What the hell just happened?"

Amy also peered out, noting the strange setting they're in, she asked, "Where are we?" The Doctor looked at the Ponds. "Nothing to worry about Rory, just saying good-bye to an old friend of mine." The Doctor boarded the TARDIS and went back to work at the console, pulling that plunger, turning this dial, and twisting those things and set the TARDIS to its next journey as his companions went back to swimming. The Doctor still remembered the note…

"_**For Peace! For Sanity!"**_

"I know all too well about that Waldo. I'm sorry."


	3. Reactivation

The Doctor took off in the TARDIS. This last misadventure has left him alone and companionless again. He nearly lost Amy and Rory to a Minotaur in a starship. Granted it wasn't totally the Minotaur's fault, but the fact was that it killed several innocent people, and he wouldn't know what he would do if Rory or Amy were to be killed.

"Good bye…Williams." he whispered to himself as he left to travel a bit more. The Doctor didn't know quite what to do now, "Perhaps I could visit H.P. Lovecraft again…nah, good writer, ok man, terrible companion, couldn't see the beauty in anything. Percy Shelley? No…constantly forcing all of his pamphlets onto me…but I did like his play about Prometheus…"

Another scanner went off. "Oh now what?" questioned The Doctor, facing the screen towards him. "What? Another Spacial-Chronotonic Reversal Wave? But how? Must be on of Franz's older ones, let's see the date."

He clicked a few buttons to see the time the Waves were released. "OK, now let's see what they are?…Blimey…" The Doctor started rushing around the console, twisting dials, pulling levers, pushing buttons, and poking that thing that beeps occasionally, and was off to France after all this time.

'The waves are coming from 2010..._someone has turned the Quantum Computer back on_!'

Jeremie got up out of bed, the last X.A.N.A. attack being averted. He yawned and stretched. Since it was Saturday, he and his friends only had classes in the mornings. "Well I better get ready," he muttered groggily.

He got dressed, went to the bathroom to brush his teeth and left for the cafeteria to meet up with the others.

The Doctor aimed the coordinates to the old Factory where the computer was stored. He pushed the button to go down only to notice a keypad now. "Damn." he pulled out his sonic-screwdriver and unlocked the elevator. He slipped in the machine and hit the down button repeatedly. "Come on Come on! I have to get down there!"

Aelita was awoken from a disturbing dream, involving X.A.N.A., some humanoid robots, with rotten humans corpses, 1.5m tall tanks, and a mysterious person, who knew the answer to…something, the dream was fading from her memory, the only other things she could remember was that she and her friends were involved.

The Doctor's fears were confirmed, the computer was standing tall and mighty before him. This reminded him of Percy Shelley again, a poem he wrote, "…Look upon my works, ye mighty, and despair…" Well, I'll admit, I'm a tad nervous that this is back online."

He walked towards the computer and grabbed the lever, "Well, time to shut you down again!" the Doctor said with faux-cheerfulness. "What's done is now done."

Jeremie turned on his laptop, which he placed on the table, since he was done with breakfast, and was about to scan Lyoko for activated towers, or to find new Replikas. But nothing came up, the scanning screen said, "Malfunction." "What the hell?" Jeremie asked, getting Odd's attention as well as Aelita's. "What's the matter Einstein?"

"The Super Scan, it's nothing's showing up." Jeremie answered, hitting the buttons again, to see if maybe he made a mistake. Aelita, "Isn't that a good thing?" Jeremie turned to the pink haired girl and answered, "No, I mean, literally nothing is here, not even inactive towers."

Their friends, Ulrich and Yumi joined, in and were quickly put up to speed. "Do you think it's some form of attack?" Ulrich quizzed in.

The Doctor sighed, "Well, that's that."

In the internet, X.A.N.A. detected something wrong with his main focusing unit and the digital dimension LYOKO. 'The supercomputer was deactivated' it thought, 'I can't allow that to happen, I still need it to lure out Waldo Schaeffer with Aelita.'

So he used the security camera to look in the supercomputer room and saw a raggedy man walking back into the elevator, 'Why is this man so familiar?'

X.A.N.A. quickly went through all the databases it could, only to find nothing about this man. Regardless he had to reactivate the supercomputer and get rid of this man, he'll have to kill the man later, but for now it had bigger fish to fry.

As The Doctor got in the elevator, pressed the up button and doors began to close, he witnessed the switch snap back on, "What?!" he was about to stop the elevator, only for elevator to slam shut, and move faster than it ever could back to the upper levels.

The super scan gave out a muffled beep, as it was hidden in Jeremie's backpack. Jeremie's eyes darted towards his bag, hoping no one noticed it. Luckily for him, class was over and they had the rest of the day off.

He looked on the screen and found that a tower was activated…but just as quickly deactivated itself.

"I wonder what that was? Did X.A.N.A. just decided against attacking? No, X.A.N.A. has no regret. So I must wonder…"

The Doctor slammed on the button to go down again, muttering, "Damn, damn, damn…" He pulled out the sonic screwdriver, and that didn't even work.

He quickly rushed to the TARDIS and took out a scanner, a strange contraption the size of an earthly cell phone, covered in wires, switches and dials. He flicked a few switches and the device exploded once it pointed to the elevator. "Well that's not good. Seems to be a program materialized from digital data, enabling someone to block out even my sonic screwdriver. Fortunately I know this'll take energy, can't be permanent."

He turned back to the TARDIS, shouting to the elevator, "I'll be back!" As he stepped in he saw kids running down the bridge. "Oh no!" he muttered running in and started pushing buttons, pulling levers and pushing more buttons.

The Doctor took comfort in the familiar sound of TARDIS taking off, only to realize one thing. The doors were wide open. "No!" he whispered, peering his head out the door, the kids have taken notice and grabbed the ropes to swing down.

He was about to close the doors when one girl caught his eyes, a girl with green eyes, and short pink hair.

'Aelita?' The Doctor shook his head and slammed the doors shut and locked them, as the TARDIS was starting to dematerialize.

The five ran where the little blue box once stood, now looking up and down to see and understand what the hell just happened.

Dumbfounded, the five said nothing, just looking up and down for whatever it was that was there for a short moment in time. 'It looked like a '60's police box,' thought Aelita.

Jeremie rushed to the elevator and pushed the down button, the elevator opening with some sort of resistance. "Come on, we have to check something." The other four followed behind their young leader to the computer interface.

Jeremie's fingers ran over the keys in a matter of seconds, accessing the security cameras. "Now, let's see who came here and how that police box got here…assuming it didn't come the same way it left."

Several windows opened up.

The video from the first screen was staring at the entryway. As amazing as watching a police box vanish, it was more so seeing it materialize out of nowhere. "Well," Jeremie said, "That answers that question."

The video showed a raggedy man rush to the elevator, he pulled out a tool, the doors unlocked and hit the down button. The third screen showed the man in the elevator, impatiently tapping his foot, muttering to himself (the cameras didn't pick up the voice), before going to the supercomputer room, the next window.

The man looked it over then pulled the lever down, shutting the machine off. As he walked away a tendril of black smoke switched the machine back on and shoved the man in the elevator and send it going up, before locking it down.

"So who is he?" questioned Odd, not understanding what was happening.

The Doctor slid the levers, twisting knobs and pulling down levers to send the TARDIS on autopilot. "Well girl," he said, "Take me somewhere so I can wrap my head around this thank you you're beautiful."

He leaned on the console, still surprised of who he saw, 'Aelita. Waldo's daughter. But how?' Almost immediately, the TARDIS landed. "What the?"

The Doctor looked at one of the many screens and found that he was…exactly one day ahead of time. He looked above him, at the TARDIS and asked, "Really? Well as long as I'm here, I guess I should make the most of it."

He opened the door, peered out, checked both sides out and stepped out, locking the doors behind him. He looked around and saw exactly where he landed. "Kadic Academy. Franz's old school." Nostalgia wept over the Doctor as he went past the gate, and onto the campus grounds. "Heh, I remember that scratch in the wall, I made that when the TARDIS landed her for the first time, the look on Franz's face!"

A large, powerful, meaty hand grabbed his arm and forced it behind him, "Who are you? Don't you know trespassing is a crime punishable with time in prison?"

"And who are y-…Jim! Oh I remember you! You were just a kid, but still! Great to see you!" The Doctor laughed, remembering Jim Morales from his time at school.

"What, how do you know me?" the man asked. The Doctor laughed a little, "Right, you wouldn't remember me, I was a friend of your science teacher, I visited him and saw you leave the class."

Jim just sort of accepted the excuse and continued with, "Alright, but you're still trespassing on federal property."

"No he's not!" declared a feminine voice from behind.

The two turned and found an attractive woman, with curly blonde hair, wearing dark pants, a white shirt with a large leather belt around her waist and stomach. "Hello sweetie."


End file.
